Comparative transcriptomic analysis of in vivo–derived and IVF porcine embryos at the 4-cell, blastocyst, and hatched blastocyst stages

Early embryonic development is highly sensitive to both developmental stage and culture environment, and in vitro fertilization (IVF) is known to induce transcriptional and epigenetic alterations that may compromise embryo quality and developmental competence. To systematically characterize stage-specific and origin-dependent transcriptional differences, we performed RNA sequencing of porcine embryos derived in vivo and by IVF at key preimplantation stages. Transcriptomes were generated from in vivo–derived blastocysts and hatched blastocysts, IVF-derived blastocysts and hatched blastocysts, as well as IVF-derived 4-cell embryos. Comparative analyses enable the dissection of transcriptional programs associated with early cleavage, blastocyst formation, hatching, and culture-induced perturbations. This dataset provides a comprehensive resource for investigating developmental stage transitions, IVF-associated transcriptional dysregulation, and molecular determinants of embryo quality during porcine preimplantation development. Overall design: RNA-seq was performed on porcine preimplantation embryos collected at defined developmental stages. Experimental groups included: (i) in vivo–derived blastocysts, (ii) in vivo–derived hatched blastocysts, (iii) IVF-derived blastocysts, (iv) IVF-derived hatched blastocysts, and (v) IVF-derived 4-cell embryos. Total RNA was extracted from pooled embryos within each group and subjected to high-throughput RNA sequencing. The resulting transcriptomic profiles were used to compare developmental stage–dependent gene expression dynamics and to assess the impact of IVF culture conditions on embryonic transcriptional programs.